Revolutionising Bacteriology to Improve Treatment Outcomes and Antibiotic Stewardship

Abstract

Laboratory investigation of bacterial infections generally takes two days: one to grow the bacteria and another to identify them and to test their susceptibility. Meanwhile the patient is treated empirically, based on likely pathogens and local resistance rates. Many patients are over-treated to prevent under-treatment of a few, compromising antibiotic stewardship. Molecular diagnostics have potential to improve this situation by accelerating precise diagnoses and the early refinement of antibiotic therapy. They include: (i) the use of 'biomarkers' to swiftly distinguish patients with bacterial infection, and (ii) molecular bacteriology to identify pathogens and their resistance genes in clinical specimens, without culture. Biomarker interest centres on procalcitonin, which has given good results particularly for pneumonias, though broader biomarker arrays may prove superior in the future. PCRs already are widely used to diagnose a few infections (e.g. tuberculosis) whilst multiplexes are becoming available for bacteraemia, pneumonia and gastrointestinal infection. These detect likely pathogens, but are not comprehensive, particularly for resistance genes; there is also the challenge of linking pathogens and resistance genes when multiple organisms are present in a sample. Next-generation sequencing offers more comprehensive profiling, but obstacles include sensitivity when the bacterial load is low, as in bacteraemia, and the imperfect correlation of genotype and phenotype. In short, rapid molecular bacteriology presents great potential to improve patient treatments and antibiotic stewardship but faces many technical challenges; moreover it runs counter to the current nostrum of defining resistance in pharmacodynamic terms, rather than by the presence of a mechanism, and the policy of centralising bacteriology services.

Antimicrobial resistance genes and modelling of treatment failure in bacterial vaginosis: clinical study of 289 symptomatic women

“…Patient outcome predictions derived from targeted sequence data of AMR genes may be imperfect owing to the multifactorial nature of drug resistance (Livermore & Wain, 2013;Tuite et al, 2014). The sources of resistance may be unknown, causing unexpected treatment failure, as AMR gene analysis may create false-positive or falsenegative results.…”

“…The most common method for diagnosis of infection and the presence of AMR genes, bacteriologic culturing, is slow and fails to grow the majority of pathogens now known to be present within microbiomes (Livermore & Wain, 2013). In a recent report, cancer patients with known bacteraemia had positive cultures in only 30-40 % of cases (Guido et al, 2012).…”

“…Incomplete definition of the microbiome is of greatest concern with AMR genes owing to the inability to assess all genes that contribute to resistance, as well as inability to identify resistance arising from mutation. Livermore & Wain (2013) noted that only a comprehensive test can replace existing methods of detection and antibiotic resistance. NGS fulfils these demands by avoiding non-comprehensive testing and its associated ascertainment bias, providing AMR data, and delivering quantitative as well as qualitative data on relative bacterial loads.…”

In vitro diagnosis of sepsis: a review

“…137 Currently, the next-generation sequencing (NGS) technology (eg, Illumina MiSeq) represents a new challenge to identify and genotype viable, dead, and viable but nonculturable pathogens, and antibiotic resistance markers, and it provides significant input to scientific discovery due to its cheap cost and fast turnaround. 92,139,140 The biggest challenge in applying NGS to BSIs is the detection of very small amounts of pathogen nucleic acid in the vast excess of human genomic DNA.…”

Automated Broad-Range Molecular Detection of Bacteria in Clinical Samples

“…Its advantages include the ability to simultaneously detect multiple species and the universal nature of the system: while selective medium may be employed to single out specific species, nonselective medium incubated under different conditions can sustain a very broad range of bacteria, which obviates having to decide in advance which specific microbe(s) should be sought. The most notable drawbacks of culture for clinical application are the long time needed for bacteria to grow (1), the inability to culture bacteria after patients have received antibiotics, and the inability to detect bacterial species that are refractory to cultivation.…”